Our long-term objective is to understand how genes control natural variation in complex phenotypes and how these phenotypes evolve. This continuing project will investigate the genetic, developmental and molecular basis of naturally occurring variation for complex morphological traits using maize as the model system. Since traits such as blood pressure and body weight, which influence susceptibility to disease in humans, are complex, a better understanding of the inheritance of complex traits in experimental organisms like maize will facilitate the treatment and management of human disease. It is crucial to conduct studies of complex traits in experimental organisms like maize since confirmation of working hypotheses by transformation, controlled crosses and other analyses cannot be done in humans. Our specific aims during the proposed project are as follows. (1) We will do map-based cloning of teosinte glume architecture1 (tga1), a quantitative trait locus (QTL) controlling a complex phenotype in maize. (2) We will test whether several cloned QTL candidate genes are the QTL in question by using transformation and genetic complementation tests. These candidates include teosinte branched1, the maize homolog (zfl2) of the Arabidopsis leafy gene, tga1, and a maize MADS-box gene (zmb1). (3) We will perform molecular and developmental characterization of the genes that represent QTL with an emphasis on comparing the developmental effects of alternate naturally occurring alleles. (4) We will analyze naturally occurring functional variation at the QTL candidate genes using association studies. Our emphasis in these experiments will be on the use of large population sizes, screening multiple polymorphisms across the genes, and testing for epistatic interactions among the polymorphisms. (5) Finally, we will analyze the patterning of genetic diversity in genomic regions that have experienced recent and strong selective sweeps to understand how the genome responds to past selective pressure.